Methods for diagnosing irritable bowel syndrome

Abstract

The present invention discloses a method for diagnosing Irritable Bowel Syndrome (IBS) in a test sample by determining the level of several bacterial taxa in the test sample, comparing this level with the levels of those bacterial taxa in a control sample, and relating the level to a diagnosis of IBS. Additionally, the present invention provides a method for treatment of IBS based on said diagnosis. Also, the invention provides a method for subtyping IBS in a test sample.

Description

FIELD OF THE INVENTION[0001]The present invention is in the field of microbiology and gastrointestinal health, and relates to the use of the gastrointestinal microbiota as a biomarker for intestinal aberrations, notably Irritable Bowel Syndrome.BACKGROUND[0002]The gastro-intestinal tract is colonized since birth by complex communities of microbes, including bacteria, archaea and fungi, that develop in time and space. These microbial communities were collectively termed gut microflora in previous times but are now known as gut microbiota that is of a highly complex nature. (Rajilic-Stojanovic et al. 2007. Environ Microbiol 9: 2125-2136) The gut microbiota is involved in a variety of metabolic functions, such as the processing of food components that are not digested by the host, the synthesis of vitamins and the production of short chain fatty acids. However, in recent years it has been established that gut microbes interact with the host cells resulting in modulation of host process...

AI Technical Summary

Benefits of technology

[0030]In an embodiment, in step iiia) an increased level of nucleic acids from said test sample, said nucleic acids being capable of hybridising to nucleic acid sequences selected from the nucleic acid sequences of SEQ ID Nos:1-27, 70-71, 73-77, 99-100, or derivatives or fragment

Problems solved by technology

Furthermore, IBS is associated with a high rate of absenteeism from work, a significant impairment in quality of life and substantial health care costs.

While the diagnosis of IBD is based on non-invasive diagnostic procedures as the presence of inflammatory biomarkers in the blood, imaging diagnostics and endoscopic observations (including histology of mucosal specimens), IBS is much harder to diagnose.

This makes the diagnosis of IBS a rather undefined ‘exclusion diagnosis’ and relatively expensive.

However, no clear picture emerges from these studies as to what are the specific microbes or microbial groups that differ between IBS and healthy subjects.

This is partly caused by the fact that in many cases use is made of culturing techniques to identify microbes, where it is well known that many of the intestinal microbes can not been cultured, and cultivation therefore is known to give significant biases.

However, none of Ruminococcus sp., Bacteroides sp., and Clostridium sp. are methane-producing organisms.

While some differences were observed in 3 of the over 15 fractions, this approach is not quantitative and known to be affected by cloning bias.

Moreover, the used approach includes a density gradient centrifugation step to fractionate the DNA samples according to their G+C content that is not applicable for routine diagnostics.

Moreover, these conflicting results can also be caused by the heterogeneity of IBS with respect to etiology, pathophysiology and symptomatology.

A study based on DGGE analysis suggested reduced temporal stability in IBS subjects but used visual inspection and did not correct for the use of antibiotics (Mattö et al., 2005, supra).

The methods of DGGE analysis due to their low resolution however lead to inconsistent results and outcomes that are notoriously difficult to reproduce.

Finally, the methods based on DGGE are laborious, time-consuming and have significant gel to gel variations and require relatively long processing times—hence they can not be used as a routine diagnostic tool.

This limits any clinical application as a general diagnostic tool for IBS.

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